Calcium in PDB 6q8g: Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution

Protein crystallography data

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution, PDB code: 6q8g was solved by S.Baeriswyl, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.92 / 1.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.445, 72.085, 123.593, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution (pdb code 6q8g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution, PDB code: 6q8g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q8g

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Calcium binding site 1 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:13.1
occ:1.00
 OD1 A:ASP99 2.4 17.8 1.0
OD1 A:ASP101 2.4 13.4 1.0
OE2 A:GLU95 2.4 14.2 1.0
OD2 A:ASP104 2.4 12.4 1.0
OE1 A:GLU95 2.5 13.7 1.0
O3 E:ZDC1 2.5 14.3 1.0
O4 E:ZDC1 2.5 14.2 1.0
OD1 A:ASP104 2.6 12.2 1.0
CD A:GLU95 2.7 13.9 1.0
CG A:ASP104 2.9 11.8 1.0
C4 E:ZDC1 3.3 14.4 1.0
C3 E:ZDC1 3.4 14.4 1.0
CG A:ASP99 3.4 17.3 1.0
CG A:ASP101 3.4 14.1 1.0
OD2 A:ASP99 3.7 17.0 1.0
CA A:CA302 3.7 12.4 1.0
OD2 A:ASP101 3.9 14.3 1.0
O A:HOH463 4.1 20.8 1.0
N A:ASP101 4.1 15.9 1.0
CG A:GLU95 4.2 13.7 1.0
OD1 A:ASP96 4.3 13.8 1.0
CB A:ASP104 4.4 11.3 1.0
N A:TYR102 4.4 12.8 1.0
N A:ASN100 4.5 16.1 1.0
N A:ASP96 4.5 12.7 1.0
CB A:ASP101 4.6 16.1 1.0
N A:GLY97 4.6 13.6 1.0
CA A:GLU95 4.7 11.5 1.0
C2 E:ZDC1 4.7 15.2 1.0
C5 E:ZDC1 4.7 15.3 1.0
CA A:ASP101 4.7 14.4 1.0
CB A:ASP99 4.7 18.1 1.0
OD1 A:ASN103 4.7 11.8 1.0
N A:ASP99 4.8 17.0 1.0
O2 E:ZDC1 4.8 14.6 1.0
CB A:GLU95 4.9 12.8 1.0
C A:ASP101 5.0 13.5 1.0
C A:ASP99 5.0 17.4 1.0
CG A:ASP96 5.0 12.2 1.0

Calcium binding site 2 out of 8 in 6q8g

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Calcium binding site 2 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:12.4
occ:1.00
 OD1 A:ASN103 2.3 11.8 1.0
O A:ASN21 2.4 13.2 1.0
OD1 A:ASP104 2.4 12.2 1.0
OD2 A:ASP101 2.4 14.3 1.0
O B:GLY114 2.4 14.3 1.0
O2 E:ZDC1 2.5 14.6 1.0
O3 E:ZDC1 2.5 14.3 1.0
OD1 A:ASP101 3.1 13.4 1.0
CG A:ASP101 3.1 14.1 1.0
C3 E:ZDC1 3.4 14.4 1.0
CG A:ASN103 3.4 11.0 1.0
C B:GLY114 3.4 14.9 1.0
C2 E:ZDC1 3.4 15.2 1.0
C A:ASN21 3.6 11.7 1.0
CG A:ASP104 3.6 11.8 1.0
OXT B:GLY114 3.6 17.7 1.0
CA A:CA301 3.7 13.1 1.0
C4 E:ZDC1 3.8 14.4 1.0
ND2 A:ASN103 3.8 13.3 1.0
CB A:ASN21 4.1 11.8 1.0
CA A:ASP104 4.2 10.4 1.0
N A:ASP104 4.3 11.3 1.0
CA A:SER22 4.4 13.5 1.0
N A:SER22 4.4 12.5 1.0
O4 E:ZDC1 4.5 14.2 1.0
OD2 A:ASP104 4.5 12.4 1.0
C A:ASN103 4.5 10.8 1.0
CB A:ASP104 4.5 11.3 1.0
CA A:ASN21 4.5 11.7 1.0
OD2 A:ASP99 4.5 17.0 1.0
O A:HOH456 4.5 25.7 1.0
CB A:ASP101 4.6 16.1 1.0
CB A:SER22 4.7 12.3 1.0
CB A:ASN103 4.7 11.6 1.0
C1 E:ZDC1 4.8 15.8 1.0
CA B:GLY114 4.8 15.2 1.0
O A:ASN103 4.8 11.1 1.0
N A:ASN103 4.9 11.4 1.0
CA A:ASN103 4.9 11.6 1.0
O5 E:ZDC1 5.0 14.5 1.0

Calcium binding site 3 out of 8 in 6q8g

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Calcium binding site 3 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:10.8
occ:1.00
 OD1 B:ASN103 2.3 10.2 1.0
OD1 B:ASP104 2.3 11.2 1.0
O B:ASN21 2.4 11.2 1.0
OD2 B:ASP101 2.4 11.8 1.0
O A:GLY114 2.4 11.9 1.0
O2 F:ZDC1 2.5 12.3 1.0
O3 F:ZDC1 2.5 12.1 1.0
OD1 B:ASP101 3.0 11.5 1.0
CG B:ASP101 3.1 12.0 1.0
CG B:ASN103 3.4 9.6 1.0
C3 F:ZDC1 3.4 12.4 1.0
C A:GLY114 3.4 12.4 1.0
C2 F:ZDC1 3.4 12.7 1.0
C B:ASN21 3.6 11.0 1.0
CG B:ASP104 3.6 10.6 1.0
OXT A:GLY114 3.6 13.9 1.0
CA B:CA301 3.7 11.2 1.0
ND2 B:ASN103 3.7 11.6 1.0
C4 F:ZDC1 3.8 12.8 1.0
CB B:ASN21 4.1 10.3 1.0
CA B:ASP104 4.2 10.2 1.0
N B:ASP104 4.3 10.0 1.0
CA B:SER22 4.4 12.3 1.0
N B:SER22 4.4 11.6 1.0
OD2 B:ASP104 4.4 11.1 1.0
O4 F:ZDC1 4.4 12.7 1.0
CB B:ASP104 4.5 10.2 1.0
O B:HOH454 4.5 23.0 1.0
OD2 B:ASP99 4.5 14.7 1.0
C B:ASN103 4.5 10.3 1.0
CA B:ASN21 4.5 10.6 1.0
CB B:ASP101 4.5 13.4 1.0
CB B:SER22 4.6 11.7 1.0
CB B:ASN103 4.7 10.4 1.0
CA A:GLY114 4.8 12.5 1.0
C1 F:ZDC1 4.8 13.7 1.0
O B:ASN103 4.8 10.2 1.0
N B:ASN103 4.9 9.8 1.0
CA B:ASN103 5.0 9.9 1.0
OD1 B:ASP99 5.0 15.6 1.0

Calcium binding site 4 out of 8 in 6q8g

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Calcium binding site 4 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:11.2
occ:1.00
 OD1 B:ASP99 2.4 15.6 1.0
OD1 B:ASP101 2.4 11.5 1.0
OD2 B:ASP104 2.4 11.1 1.0
OE2 B:GLU95 2.4 11.8 1.0
OE1 B:GLU95 2.5 11.3 1.0
O3 F:ZDC1 2.5 12.1 1.0
O4 F:ZDC1 2.5 12.7 1.0
OD1 B:ASP104 2.6 11.2 1.0
CD B:GLU95 2.8 11.3 1.0
CG B:ASP104 2.9 10.6 1.0
C4 F:ZDC1 3.3 12.8 1.0
CG B:ASP99 3.4 15.7 1.0
C3 F:ZDC1 3.4 12.4 1.0
CG B:ASP101 3.4 12.0 1.0
OD2 B:ASP99 3.7 14.7 1.0
CA A:CA303 3.7 10.8 1.0
OD2 B:ASP101 3.9 11.8 1.0
O B:HOH460 4.1 22.0 1.0
N B:ASP101 4.2 13.2 1.0
OD1 B:ASP96 4.3 13.7 1.0
CG B:GLU95 4.3 12.0 1.0
CB B:ASP104 4.4 10.2 1.0
N B:TYR102 4.5 10.7 1.0
N B:ASP96 4.5 11.5 1.0
N B:ASN100 4.5 14.3 1.0
N B:GLY97 4.6 13.1 1.0
CB B:ASP101 4.6 13.4 1.0
OD1 B:ASN103 4.7 10.2 1.0
CA B:GLU95 4.7 9.9 1.0
C2 F:ZDC1 4.7 12.7 1.0
CB B:ASP99 4.7 15.0 1.0
C5 F:ZDC1 4.7 14.7 1.0
CA B:ASP101 4.8 12.1 1.0
N B:ASP99 4.8 15.0 1.0
O2 F:ZDC1 4.8 12.3 1.0
CB B:GLU95 4.9 11.4 1.0
CG B:ASP96 5.0 12.1 1.0
CA B:GLY97 5.0 15.1 1.0

Calcium binding site 5 out of 8 in 6q8g

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Calcium binding site 5 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:13.7
occ:1.00
 OD1 C:ASP99 2.3 17.8 1.0
OD1 C:ASP101 2.3 14.9 1.0
OE2 C:GLU95 2.4 14.7 1.0
OD2 C:ASP104 2.4 13.6 1.0
OE1 C:GLU95 2.4 13.9 1.0
O3 G:ZDC1 2.5 14.1 1.0
O4 G:ZDC1 2.5 14.9 1.0
OD1 C:ASP104 2.6 13.7 1.0
CD C:GLU95 2.7 13.7 1.0
CG C:ASP104 2.9 13.5 1.0
C4 G:ZDC1 3.3 15.2 1.0
CG C:ASP99 3.4 17.7 1.0
C3 G:ZDC1 3.4 14.6 1.0
CG C:ASP101 3.4 14.3 1.0
OD2 C:ASP99 3.7 16.6 1.0
CA C:CA302 3.7 13.6 1.0
OD2 C:ASP101 4.0 14.3 1.0
O C:HOH477 4.1 22.1 1.0
N C:ASP101 4.1 15.9 1.0
OD1 C:ASP96 4.2 16.6 1.0
CG C:GLU95 4.2 14.2 1.0
CB C:ASP104 4.4 14.7 1.0
N C:TYR102 4.5 13.0 1.0
N C:ASN100 4.5 16.7 1.0
N C:ASP96 4.5 13.1 1.0
CB C:ASP101 4.6 14.8 1.0
N C:GLY97 4.6 14.9 1.0
CA C:GLU95 4.7 13.1 1.0
CB C:ASP99 4.7 17.9 1.0
C2 G:ZDC1 4.7 14.3 1.0
CA C:ASP101 4.7 14.8 1.0
C5 G:ZDC1 4.7 17.3 1.0
OD1 C:ASN103 4.8 13.5 1.0
N C:ASP99 4.8 17.2 1.0
O2 G:ZDC1 4.8 14.8 1.0
CB C:GLU95 4.9 12.5 1.0
C C:ASP99 4.9 17.3 1.0
CG C:ASP96 4.9 15.4 1.0
C C:ASP101 5.0 13.4 1.0

Calcium binding site 6 out of 8 in 6q8g

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Calcium binding site 6 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:13.6
occ:1.00
 O C:ASN21 2.3 15.1 1.0
OD1 C:ASN103 2.3 13.5 1.0
OD1 C:ASP104 2.4 13.7 1.0
OD2 C:ASP101 2.4 14.3 1.0
O D:GLY114 2.4 14.9 1.0
O2 G:ZDC1 2.5 14.8 1.0
O3 G:ZDC1 2.5 14.1 1.0
CG C:ASP101 3.1 14.3 1.0
OD1 C:ASP101 3.1 14.9 1.0
CG C:ASN103 3.4 13.1 1.0
C3 G:ZDC1 3.4 14.6 1.0
C D:GLY114 3.4 17.4 1.0
C2 G:ZDC1 3.4 14.3 1.0
C C:ASN21 3.5 14.9 1.0
CG C:ASP104 3.6 13.5 1.0
OXT D:GLY114 3.6 19.3 1.0
CA C:CA301 3.7 13.7 1.0
ND2 C:ASN103 3.8 13.6 1.0
C4 G:ZDC1 3.8 15.2 1.0
CB C:ASN21 4.1 13.8 1.0
CA C:ASP104 4.2 13.0 1.0
N C:ASP104 4.3 12.2 1.0
CA C:SER22 4.4 15.9 1.0
N C:SER22 4.4 15.2 1.0
O4 G:ZDC1 4.5 14.9 1.0
OD2 C:ASP104 4.5 13.6 1.0
C C:ASN103 4.5 12.9 1.0
O C:HOH436 4.5 24.5 1.0
CB C:ASP104 4.5 14.7 1.0
CA C:ASN21 4.5 14.4 1.0
CB C:ASP101 4.5 14.8 1.0
OD2 C:ASP99 4.5 16.6 1.0
CB C:SER22 4.6 16.9 1.0
CB C:ASN103 4.7 12.9 1.0
C1 G:ZDC1 4.8 16.1 1.0
CA D:GLY114 4.8 17.1 1.0
O C:ASN103 4.8 13.2 1.0
N C:ASN103 4.9 11.8 1.0
CA C:ASN103 4.9 13.3 1.0
O5 G:ZDC1 5.0 15.7 1.0

Calcium binding site 7 out of 8 in 6q8g

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Calcium binding site 7 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:15.7
occ:1.00
 O D:ASN21 2.3 17.2 1.0
OD1 D:ASN103 2.3 15.4 1.0
OD1 D:ASP104 2.4 16.4 1.0
OD2 D:ASP101 2.4 17.6 1.0
O2 C:ZDC303 2.4 17.2 1.0
O C:GLY114 2.4 17.0 1.0
O3 C:ZDC303 2.5 17.8 1.0
OD1 D:ASP101 3.1 17.3 1.0
CG D:ASP101 3.1 18.1 1.0
CG D:ASN103 3.4 14.3 1.0
C3 C:ZDC303 3.4 18.2 1.0
C2 C:ZDC303 3.4 18.4 1.0
C C:GLY114 3.4 18.5 1.0
C D:ASN21 3.5 16.3 1.0
CG D:ASP104 3.6 15.8 1.0
OXT C:GLY114 3.6 20.5 1.0
CA D:CA201 3.7 16.7 1.0
ND2 D:ASN103 3.8 15.9 1.0
C4 C:ZDC303 3.8 18.8 1.0
CB D:ASN21 4.1 15.6 1.0
CA D:ASP104 4.2 14.5 1.0
N D:ASP104 4.3 14.0 1.0
CA D:SER22 4.4 17.9 1.0
N D:SER22 4.4 16.4 1.0
OD2 D:ASP104 4.4 16.2 1.0
O4 C:ZDC303 4.4 17.6 1.0
CB D:ASP104 4.5 15.7 1.0
C D:ASN103 4.5 14.7 1.0
CA D:ASN21 4.5 15.8 1.0
OD2 D:ASP99 4.5 20.5 1.0
O D:HOH358 4.5 28.4 1.0
CB D:ASP101 4.5 18.9 1.0
CB D:SER22 4.6 18.3 1.0
CB D:ASN103 4.7 14.4 1.0
C1 C:ZDC303 4.8 19.0 1.0
CA C:GLY114 4.8 16.8 1.0
O D:ASN103 4.8 14.4 1.0
N D:ASN103 4.9 14.0 1.0
CA D:ASN103 4.9 13.9 1.0
OD1 D:ASP99 5.0 20.3 1.0
O5 C:ZDC303 5.0 19.3 1.0

Calcium binding site 8 out of 8 in 6q8g

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Calcium binding site 8 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:16.7
occ:1.00
 OD1 D:ASP99 2.3 20.3 1.0
OD1 D:ASP101 2.4 17.3 1.0
OE1 D:GLU95 2.4 17.7 1.0
OD2 D:ASP104 2.4 16.2 1.0
O3 C:ZDC303 2.4 17.8 1.0
O4 C:ZDC303 2.5 17.6 1.0
OE2 D:GLU95 2.5 17.1 1.0
OD1 D:ASP104 2.6 16.4 1.0
CD D:GLU95 2.8 18.2 1.0
CG D:ASP104 2.9 15.8 1.0
C4 C:ZDC303 3.3 18.8 1.0
CG D:ASP99 3.4 19.1 1.0
C3 C:ZDC303 3.4 18.2 1.0
CG D:ASP101 3.4 18.1 1.0
OD2 D:ASP99 3.7 20.5 1.0
CA C:CA304 3.7 15.7 1.0
OD2 D:ASP101 3.9 17.6 1.0
O D:HOH368 4.0 25.3 1.0
N D:ASP101 4.1 17.7 1.0
OD1 D:ASP96 4.2 19.1 1.0
CG D:GLU95 4.3 18.1 1.0
CB D:ASP104 4.4 15.7 1.0
N D:TYR102 4.5 15.9 1.0
N D:ASP96 4.5 15.7 1.0
N D:ASN100 4.5 20.1 1.0
N D:GLY97 4.6 17.9 1.0
CB D:ASP101 4.6 18.9 1.0
CA D:GLU95 4.7 14.3 1.0
C2 C:ZDC303 4.7 18.4 1.0
CB D:ASP99 4.7 21.2 1.0
CA D:ASP101 4.7 17.2 1.0
OD1 D:ASN103 4.7 15.4 1.0
C5 C:ZDC303 4.8 19.7 1.0
N D:ASP99 4.8 20.0 1.0
O2 C:ZDC303 4.8 17.2 1.0
CB D:GLU95 4.9 16.1 1.0
CG D:ASP96 4.9 18.7 1.0
C D:ASP99 5.0 20.0 1.0
C D:ASP101 5.0 16.2 1.0

Reference:

S.Baeriswyl, B.H.Gan, T.N.Siriwardena, R.Visini, M.Robadey, S.Javor, A.Stocker, T.Darbre, J.L.Reymond. X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047
Page generated: Sat Dec 12 07:27:07 2020

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